Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
Yuichi Taniguchi,Paul J. Choi,Gene-Wei Li,Huiyi Chen,Mohan Babu,Jeremy Hearn,Andrew Emili,X. Sunney Xie +7 more
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TLDR
System-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size.Abstract:
Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described by the gamma distribution with two fitting parameters which, at low expression levels, have clear physical interpretations as the transcription rate and protein burst size. At high expression levels, the distributions are dominated by extrinsic noise. We found that a single cell's protein and mRNA copy numbers for any given gene are uncorrelated.read more
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Using variability in gene expression as a tool for studying gene regulation
Olivia Padovan-Merhar,Arjun Raj +1 more
TL;DR: It is believed that use of variability can provide new biological insights into different aspects of transcriptional control and can provide a powerful complementary approach to that of existing techniques.
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Chromosome-centric approach to overcoming bottlenecks in the Human Proteome Project
Alexander I. Archakov,Victor G. Zgoda,Arthur T. Kopylov,Stanislav N. Naryzhny,Alexey Chernobrovkin,Elena A. Ponomarenko,Andrey Lisitsa +6 more
TL;DR: The authors here discuss approaches to overcome three bottlenecks in the implementation of the HPP: the insufficient sensitivity of proteomic technologies, the dynamic nature of the proteome and its instability over time.
Journal ArticleDOI
A Rapid Response Thin-Film Plasmonic-Thermoelectric Light Detector
Ying Pan,Giulia Tagliabue,Giulia Tagliabue,Hadi Eghlidi,Christian Höller,Susanne Dröscher,Guo Hong,Dimos Poulikakos +7 more
TL;DR: A hybrid detector for visible and near-infrared light achieving response times of the order of 100 milliseconds, almost four times shorter than the same thermoelectric device covered with a conventional absorber and an almost two times higher light-to-electricity efficiency upon replacing the conventional absorbers with a plasmonic absorber.
Journal ArticleDOI
Intracellular Signaling by the comRS System in Streptococcus mutans Genetic Competence
Simon A. M. Underhill,Robert C. Shields,Justin R. Kaspar,Momin Haider,Robert A. Burne,Stephen J. Hagen +5 more
TL;DR: It is demonstrated that endogenously produced ComS can enable ComRS to activate comX without requiring processing, export, or import, which provides insight into intracellular mechanisms that generate noise and heterogeneity in S. mutans competence.
Journal ArticleDOI
Stochastic timing in gene expression for simple regulatory strategies
Alma Dal Co,Marco Cosentino Lagomarsino,Marco Cosentino Lagomarsino,Michele Caselle,Matteo Osella +4 more
TL;DR: The analytical estimates and simulations show that, for an induced gene, timing variability is minimal if the threshold level of expression is approximately half of the steady-state level, which lays a framework for understanding stochasticity of endogenous systems such as the cell cycle, as well as for the design of synthetic trigger circuits.
References
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疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
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Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Tomoya Baba,Takeshi Ara,Miki Hasegawa,Yuki Takai,Yoshiko Okumura,Miki Baba,Kirill A. Datsenko,Masaru Tomita,Barry L. Wanner,Hirotada Mori,Hirotada Mori +10 more
TL;DR: These mutants—the ‘Keio collection’—provide a new resource not only for systematic analyses of unknown gene functions and gene regulatory networks but also for genome‐wide testing of mutational effects in a common strain background, E. coli K‐12 BW25113.
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Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
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Global analysis of protein localization in budding yeast
Won-Ki Huh,James V. Falvo,Luke C. Gerke,Adam S. Carroll,Russell W. Howson,Jonathan S. Weissman,Erin K. O'Shea +6 more
TL;DR: The construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins helps reveal the logic of transcriptional co-regulation, and provides a comprehensive view of interactions within and between organelles in eukaryotic cells.
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Fabrication of microfluidic systems in poly(dimethylsiloxane)
J.C. McDonald,David C. Duffy,Janelle R. Anderson,Daniel T. Chiu,Hongkai Wu,Olivier Schueller,George M. Whitesides +6 more
TL;DR: Fabrication of microfluidic devices in poly(dimethylsiloxane) (PDMS) by soft lithography provides faster, less expensive routes to devices that handle aqueous solutions.